Multiple platform build/check report for BioC 3.22 - CHECK results for cellmigRation on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for cellmigRation on kjohnson1

To the developers/maintainers of the cellmigRation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellmigRation.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: cellmigRation

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.18.0.tar.gz

StartedAt: 2025-11-18 03:48:14 -0500 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 03:49:13 -0500 (Tue, 18 Nov 2025)

EllapsedTime: 59.5 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cellmigRation_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck’
* using R version 4.5.2 Patched (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.18.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cellmigRation’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'fixDA.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM1.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM2.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM3.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM4.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM5.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM6.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixID2.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID3.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID4.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixMSD.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixPER1.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'fixPER2.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'innerBondRaster.Rd':
  ‘i’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.18.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cellmigRation)

Tests output

cellmigRation.Rcheck/tests/runTests.Rout


R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("cellmigRation")


RUNIT TEST PROTOCOL -- Tue Nov 18 03:49:06 2025 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
cellmigRation RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.312   0.109   1.696

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.001	0.000	0.001
CellMig-class	0.014	0.001	0.015
CellMigPCA	0.698	0.021	0.799
CellMigPCAclust	0.004	0.001	0.005
CellMigPCAclustALL	0.211	0.004	0.217
CellTracker	0.008	0.001	0.009
CellTrackerMainLoop	0.003	0.006	0.015
CentroidArray	0.008	0.002	0.010
CentroidValidation	0.162	0.006	0.181
ComputeTracksStats	0.010	0.001	0.012
DetectRadii	0.001	0.000	0.001
DiAutoCor	0.453	0.005	0.539
DiRatio	0.006	0.000	0.007
DiRatioPlot	0.014	0.005	0.019
EstimateDiameterRange	0.005	0.001	0.006
FMI	0.163	0.003	0.194
FianlizeOptiParams	0.000	0.000	0.001
FilterTrackedCells	0.001	0.000	0.001
FinRes	0.216	0.004	0.223
ForwardMigration	0.313	0.002	0.322
GenAllCombos	0.001	0.001	0.001
LinearConv2	0.006	0.000	0.007
LoadTiff	0.000	0.001	0.000
MSD	0.513	0.016	0.591
MakeHypercube	0.000	0.000	0.001
MigrationStats	0.001	0.000	0.001
NextOdd	0.000	0.001	0.000
NonParallel4OptimizeParams	0.000	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.007	0.001	0.012
OptimizeParamsMainLoop	0.002	0.005	0.011
Parallel4OptimizeParams	0	0	0
ParallelTrackLoop	0.001	0.000	0.000
PerAndSpeed	0.100	0.009	0.115
PlotTracksSeparately	0.004	0.000	0.005
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.031	0.002	0.033
ThreeConditions	0.005	0.002	0.006
TrackCellsDataset	0.007	0.001	0.008
TrajectoryDataset	0.012	0.001	0.013
ValidateTrackingArgs	0.000	0.001	0.000
VeAutoCor	0.365	0.004	0.376
VisualizeCntr	0.001	0.001	0.001
VisualizeImg	0.002	0.000	0.002
VisualizeStackCentroids	0.022	0.004	0.025
WSADataset	0.004	0.001	0.004
aggregateFR	0.218	0.004	0.233
aggregateTrackedCells	0.009	0.002	0.012
bpass	0.029	0.001	0.041
circshift	0.000	0.000	0.001
cntrd	0.252	0.006	0.289
fixDA	0	0	0
fixExpName	0	0	0
fixFM1	0	0	0
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0.000	0.001	0.000
fixFM5	0	0	0
fixFM6	0	0	0
fixID1	0	0	0
fixMSD	0	0	0
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0	0	0
getAvailableAggrMetrics	0.322	0.003	0.330
getCellImages	0.098	0.387	0.577
getCellMigSlot	0.159	0.238	0.471
getCellTrackMeta	0.007	0.001	0.009
getCellTrackStats	0.010	0.002	0.016
getCellTracks	0.007	0.001	0.008
getCellsMeta	0.007	0.001	0.008
getCellsStats	0.011	0.001	0.020
getDACtable	0.911	0.012	1.127
getDiRatio	0.008	0.001	0.008
getFMItable	0.177	0.002	0.189
getForMigtable	0.202	0.003	0.263
getImageCentroids	0.009	0.002	0.011
getImageStacks	0.022	0.003	0.025
getMSDtable	1.315	0.015	1.484
getOptimizedParameters	0.007	0.001	0.008
getOptimizedParams	0.008	0.002	0.009
getPerAndSpeed	0.095	0.010	0.106
getPopulationStats	0.008	0.001	0.009
getProcessedImages	0.092	0.383	0.571
getProcessingStatus	0.007	0.002	0.009
getResults	0.238	0.006	0.266
getTracks	0.007	0.001	0.009
getVACtable	0.431	0.005	0.503
initializeTrackParams	0.000	0.000	0.001
innerBondRaster	0.001	0.000	0.001
internalPermutation	0.000	0.000	0.001
matfix	0.001	0.000	0.000
nontrivialBondTracking	0	0	0
pkfnd	0.236	0.005	0.273
plot3DAllTracks	0.001	0.000	0.001
plot3DTracks	0	0	0
plotAllTracks	0.007	0.001	0.023
plotSampleTracks	0.006	0.001	0.008
preProcCellMig	0.004	0.001	0.005
rmPreProcessing	0.034	0.002	0.035
runTrackingPermutation	0.001	0.000	0.001
setAnalyticParams	0.007	0.001	0.010
setCellMigSlot	0.013	0.001	0.017
setCellTracks	0.007	0.001	0.008
setCellsMeta	0.007	0.001	0.009
setExpName	0.012	0.001	0.018
setOptimizedParams	0.008	0.001	0.009
setProcessedImages	0.007	0.001	0.017
setProcessingStatus	0.012	0.002	0.021
setTrackedCellsMeta	0.008	0.001	0.009
setTrackedCentroids	0.009	0.002	0.016
setTrackedPositions	0.007	0.001	0.008
setTrackingStats	0.007	0.001	0.013
sinkAway	0.001	0.000	0.000
subNetworkTracking	0	0	0
track	0.003	0.000	0.004
trackHypercubeBuild	0	0	0
trackSlideProcessing	0	0	0
trackSlideWrapUp	0.001	0.000	0.000
trivialBondRaster	0.000	0.000	0.001
trivialBondTracking	0	0	0
visualizeCellTracks	0.023	0.003	0.036
visualizeTrcks	0.017	0.001	0.018
warnMessage	0	0	0
wsaPreProcessing	0.019	0.001	0.024